Table 3.

Differences in UDP-GlcNAc Binding between Chains A and B of CtLpxD Complex I versus CtLpxD Complex II.

Ct LpxD Residue and Heteroatom near UDP- GlcNAc	Corresponding EcLpxD Residue§	Possible H-bond or Polar Partner on UDP-GlcNAc	Distance in Å Complex I	Distance in Å Complex II
Chain A
F190 O		GlcNAc O4	2.67*	8.14*
Y192 N		GlcNAc O6	3.15	11.3
H247 NE2**	H239	GlcNAc O3	3.07	6.71
H247 NE2	H239	GlcNAc O7‡	5.01	2.61
H247 NE2	H239	GlcNAc N2	4.50	4.60
Q248 OE1	N240	Ribose O3	3.03	2.92
Q248 NE2	N240	Ribose O3	3.30	3.66
G265 O		GlcNAc O7‡	2.35	5.74
S266 OG	S258	Ribose O3	2.78	3.93
H284 NE2	H276	PO alpha 1	3.11	2.70
H284 NE2	H276	PO beta 2	3.34	2.53
H284 NE2	H276	GlcNAc O7‡	3.21	5.42
H284 NE2	H276	GlcNAc N2	3.19	4.69
Chain B
E32 OE2		Ribose O3	3.40	2.62
I33 N		Uracil O2	2.82	2.80
E34 OE1	Q32	Ribose O2	4.50	3.01
F43 O	F41	Uracil N3	2.93	2.68
D45 N		Uracil O4	2.82	2.78
N46 N	N44	Uracil O4	3.50	3.26
N46 ND2	N44	GlcNAc O6	8.77	3.09
N46 ND2	N44	PO beta 1	3.84	3.23
Y49 OH	Y47	PO beta 2	3.08	2.40

Distance measurements were made using PyMol (DeLano Scientific, San Carlos, CA) on pdb file 2iu8 for Complex I and 2iu9 for Complex II (14).

^§Residues subjected to site directed mutagenesis in EcLpxD; see Table 4.

^*Numbers in red highlight distance discrepancies of > 1.50 Å in the positioning of UDP-GlcNAc in Complex I versus II.

^**H247 distances are based on the proper rotamer predicted by MolProbity (52, 53).

^‡O7 is the carbonyl oxygen of the acetyl moiety.